High-throughput sequencing yields a complete mitochondrial genome of the rice thrips, Stenchaetothrips biformis (Thysanoptera: Thripidae)

Abstract Rice thrips, Stenchaetothrips biformis (Bagnall, 1913), are one of the destructive pests of rice. Here, the complete mitochondrial genome of S. biformis was sequenced using high-throughput sequencing. The mitogenome is 15,359 bp long with an A + T content of 76.94%, which contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), 2 ribosomal RNA genes (rRNAs) and 2 putative control regions (CRs). The phylogenetic analysis showed that S. biformis is closely related to Thrips imaginis and Thrips palmi. This new mitochondrial genome data can be better used to provide a basis for studies of the mitochondrial evolution of Thysanoptera.


Introduction
In eukaryotic cells, the genomes of mitochondria contain tRNAs-, rRNAs-, and protein-coding genes, whose functions appear to be universally conserved, however, the gene content, arrangement expression, and even the genomic size exhibit remarkable variation (Gray 2012). In insects, the mitochondrial genome is the most extensively researched genomic system and is used as a popular molecular marker for phylogenetic inference, identification of species origin, analysis of population structure and dynamics, molecular evolution, and so on (Cameron 2014).
Thysanoptera contains more than 5500 species, most of which are tiny and linear, a large of these species are phytophagous, and even some species are globally important crop pests. More and more thrips' mitochondria genomics are sequenced and reported, in which gene rearrangement is characteristic, such as the plague thrips, Thrips imagines; the flower thrips Frankliniella intonsa; the western flower thrips, Frankliniella occidentalis (Shao and Barker 2003;Yan et al. 2012Yan et al. , 2014. The rice thrip, Stenchaetothrips biformis, is one of the most important rice pests in Europe, South America, and Asia, which attacks in the seedling stage of rice and causes huge losses (Nugaliyadde and Heinrichs 1984). However, the full mitochondrial genome is still unknown, which limits this species' phylogeny study, species diagnostics, biogeography study, and so on. In this study, we got the complete mitochondrial genome sequence through high-throughput sequencing.

Ethics statement
The program of insect collection and experiment in the article has passed the ethical review of Animal and plant Ethics Committee of Ningbo University.

Mitochondrial genome assembly and annotation
Genomic DNA was isolated by WizardV R Genomic DNA Purification Kit according to the manufacturer's instructions. The complete mitochondrial genome of S. biformis (GenBank Accession number: ON653412) was sequenced using Illumina HiSeq 4000, and A de novo assembler soft NOVOPlasty was used to do the assembly (Dierckxsens et al. 2017). The protein-coding genes (PCGs), tRNAs, rRNAs, and 2 control regions (CRs) were analyzed by MITOS2 online webserver (Bernt et al. 2013).

Phylogenetic analysis
Sequences used in the phylogenetic analysis were obtained from the NCBI GenBank database, the "GTR þ G4" model was employed to construct a phylogenetic tree in Software Raxml-ng with 1000 bootstrap replications (Kozlov et al. 2019).
To assess the mitochondrial sequence authenticity of S. biformis and its phylogenetic position, we selected other 9  thysanopteran species to reconstruct phylogenetic tree using Raxml-ng (Huelsenbeck and Ronquist 2001;Shao and Barker 2003;Yan et al. 2012Yan et al. , 2014Liu et al. 2017;Chakraborty et al. 2018;Chen et al. 2018;Kumar et al. 2019). The analysis of phylogeny showed that S. biformis is closely related to Thrips imaginis and Thrips palmi (Figure 3).

Discussion and conclusion
In summary, we assembled the mitochondrial genome of rice thrips, S. biformis, 15,359 bp in length, whose size is middle in Thripidae species, we also found 37 genes were coded and two control regions distributed on the genome. Thrips mitochondrial genomes are marked by high rates of gene rearrangement, our results could help to understand these phenomena. The complete mitochondrial genome of S. biformis can also be better used to identify the species of Thripidae and study the evolution of Thripidae.

Author contribution
Chuan-Xi Zhang was involved in the conception and design; Qing-Ling Hu and Zhuang-Xin Ye performed experiments and data analyses; Qing-Ling Hu wrote the original manuscript; Chuan-Xi Zhang revised the manuscript. All authors reviewed and approved the final manuscript.

Disclosure statement
No potential conflict of interest was reported by the authors.

Funding
This work was funded by National key R & D plan in the 14th five years plan (2021YFD1401100).

Data availability statement
The genome sequence data that support the findings in this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/) under accession no. ON653412. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA846937, SRR19576561, and SAMN28906286, respectively.